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MCL coexpression mm9:1309: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005409!2.26e-16!47;UBERON:0004119!9.68e-16!118;UBERON:0000925!9.68e-16!118;UBERON:0006595!9.68e-16!118;UBERON:0001007!1.11e-15!116;UBERON:0001555!1.11e-15!116;UBERON:0007026!1.11e-15!116;UBERON:0000160!6.24e-15!31;UBERON:0004921!1.19e-14!114;UBERON:0005177!9.18e-14!79;UBERON:0009854!1.90e-12!23;UBERON:0009856!1.90e-12!23;UBERON:0005172!9.96e-12!49;UBERON:0005173!9.96e-12!49;UBERON:0002417!9.96e-12!49;UBERON:0000916!9.96e-12!49;UBERON:0002107!1.02e-11!22;UBERON:0007499!1.02e-11!22;UBERON:0006925!1.02e-11!22;UBERON:0009497!1.02e-11!22;UBERON:0000015!1.02e-11!22;UBERON:0002423!1.02e-11!22;UBERON:0006235!1.02e-11!22;UBERON:0008835!1.02e-11!22;UBERON:0003894!1.02e-11!22;UBERON:0004161!1.02e-11!22;UBERON:0008836!1.02e-11!22;UBERON:0009569!2.55e-11!66;UBERON:0002100!2.61e-10!90;UBERON:0002365!1.03e-09!25;UBERON:0002330!1.03e-09!25;UBERON:0000344!2.10e-09!15;UBERON:0000466!2.40e-08!79;UBERON:0001242!2.76e-08!13;UBERON:0000060!2.76e-08!13;UBERON:0001262!2.76e-08!13;UBERON:0004786!2.76e-08!13;UBERON:0003104!1.00e-07!61;UBERON:0009142!1.00e-07!61;UBERON:0004923!1.56e-07!24;UBERON:0005256!2.97e-07!45
|ontology_enrichment_uberon=UBERON:0005409!2.26e-16!47;UBERON:0004119!9.68e-16!118;UBERON:0000925!9.68e-16!118;UBERON:0006595!9.68e-16!118;UBERON:0001007!1.11e-15!116;UBERON:0001555!1.11e-15!116;UBERON:0007026!1.11e-15!116;UBERON:0000160!6.24e-15!31;UBERON:0004921!1.19e-14!114;UBERON:0005177!9.18e-14!79;UBERON:0009854!1.90e-12!23;UBERON:0009856!1.90e-12!23;UBERON:0005172!9.96e-12!49;UBERON:0005173!9.96e-12!49;UBERON:0002417!9.96e-12!49;UBERON:0000916!9.96e-12!49;UBERON:0002107!1.02e-11!22;UBERON:0007499!1.02e-11!22;UBERON:0006925!1.02e-11!22;UBERON:0009497!1.02e-11!22;UBERON:0000015!1.02e-11!22;UBERON:0002423!1.02e-11!22;UBERON:0006235!1.02e-11!22;UBERON:0008835!1.02e-11!22;UBERON:0003894!1.02e-11!22;UBERON:0004161!1.02e-11!22;UBERON:0008836!1.02e-11!22;UBERON:0009569!2.55e-11!66;UBERON:0002100!2.61e-10!90;UBERON:0002365!1.03e-09!25;UBERON:0002330!1.03e-09!25;UBERON:0000344!2.10e-09!15;UBERON:0000466!2.40e-08!79;UBERON:0001242!2.76e-08!13;UBERON:0000060!2.76e-08!13;UBERON:0001262!2.76e-08!13;UBERON:0004786!2.76e-08!13;UBERON:0003104!1.00e-07!61;UBERON:0009142!1.00e-07!61;UBERON:0004923!1.56e-07!24;UBERON:0005256!2.97e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,1.32583,0.916672,0.550971,0.645383,1.98129,0.7141,1.00112,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,0.35122,1.58083,0.345236,0.472505,0.686615,0.223823,0.572827,1.80527,1.0231,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.871288,0.629145,0.820134,0.27383,0.342638,0.56353,0.671603,0.366415,2.48719,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,1.47196,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.30995
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,1.32583,0.916672,0.550971,0.645383,1.98129,0.7141,1.00112,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,0.35122,1.58083,0.345236,0.472505,0.686615,0.223823,0.572827,1.80527,1.0231,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.871288,0.629145,0.820134,0.27383,0.342638,0.56353,0.671603,0.366415,2.48719,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,1.47196,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.540361,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;1.39154,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;2.21808,MA0017.1;1.00628,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;2.3347,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.895081,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.827788,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.00638767,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;1.19273,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.57901,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;1.49046,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;1.16221,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;1.72325,MA0144.1;0.829535,MA0145.1;0.761789,MA0146.1;0.153598,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;2.47808,MA0035.2;0.630778,MA0039.2;1.76222,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;1.81396,MA0065.2;0.763394,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;4.17224,MA0154.1;0.480757,MA0155.1;0.414701,MA0156.1;1.04798,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.881902,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.397553,MA0163.1;0.664494,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;1.83891,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}
}}

Revision as of 13:08, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:94254231..94254297,-p1@Abcc3
Mm9::chr11:94463110..94463136,-p1@Acsf2
Mm9::chr13:4278666..4278696,-p3@Akr1c12
Mm9::chr15:82451361..82451377,-p1@Cyp2d34
Mm9::chr4:102887741..102887746,-p5@Slc35d1
Mm9::chr4:102887752..102887806,-p1@Slc35d1


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0015722canalicular bile acid transport0.00788868188536945
GO:0015721bile acid and bile salt transport0.00788868188536945
GO:0015718monocarboxylic acid transport0.0157739062236469
GO:0006805xenobiotic metabolic process0.0197076607374247
GO:0009410response to xenobiotic stimulus0.0197076607374247
GO:0004033aldo-keto reductase activity0.0197076607374247



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
gastrointestinal system2.26e-1647
endoderm-derived structure9.68e-16118
endoderm9.68e-16118
presumptive endoderm9.68e-16118
digestive system1.11e-15116
digestive tract1.11e-15116
primitive gut1.11e-15116
intestine6.24e-1531
subdivision of digestive tract1.19e-14114
trunk region element9.18e-1479
digestive tract diverticulum1.90e-1223
sac1.90e-1223
abdomen element9.96e-1249
abdominal segment element9.96e-1249
abdominal segment of trunk9.96e-1249
abdomen9.96e-1249
liver1.02e-1122
epithelial sac1.02e-1122
digestive gland1.02e-1122
epithelium of foregut-midgut junction1.02e-1122
anatomical boundary1.02e-1122
hepatobiliary system1.02e-1122
foregut-midgut junction1.02e-1122
hepatic diverticulum1.02e-1122
liver primordium1.02e-1122
septum transversum1.02e-1122
liver bud1.02e-1122
subdivision of trunk2.55e-1166
trunk2.61e-1090
exocrine gland1.03e-0925
exocrine system1.03e-0925
mucosa2.10e-0915
immaterial anatomical entity2.40e-0879
intestinal mucosa2.76e-0813
anatomical wall2.76e-0813
wall of intestine2.76e-0813
gastrointestinal system mucosa2.76e-0813
mesenchyme1.00e-0761
entire embryonic mesenchyme1.00e-0761
organ component layer1.56e-0724
trunk mesenchyme2.97e-0745


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.11.39154
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.12.21808
MA0017.11.00628
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.12.3347
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.827788
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.00638767
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.19273
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.57901
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.11.49046
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.11.16221
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.11.72325
MA0144.10.829535
MA0145.10.761789
MA0146.10.153598
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.22.47808
MA0035.20.630778
MA0039.21.76222
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.21.81396
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.14.17224
MA0154.10.480757
MA0155.10.414701
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.10.397553
MA0163.10.664494
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.21.83891
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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